Completely dependent on the virus, but the pen drive is basically treated like any other hard drive and thus can be infected. Most infections tend to target the autorun.inf file on the pen drive because it is read when the pen drive is plugged in. As a technician who is constantly swapping out my pen/flash drive in and out of machines.....which can spread a virus from machine to another.....I use Panda usb vaccination. Basically it prevents changing the autorun.inf, it is free and works on all removable media.
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